Published in Genome Biol on December 23, 2010
Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand. Proc Natl Acad Sci U S A (2011) 1.46
Nitrate and ammonium lead to distinct global dynamic phosphorylation patterns when resupplied to nitrogen-starved Arabidopsis seedlings. Plant J (2012) 1.36
Arabidopsis roots and shoots show distinct temporal adaptation patterns toward nitrogen starvation. Plant Physiol (2011) 1.13
Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants. Nat Commun (2013) 1.09
Transcriptional dynamics elicited by a short pulse of notch activation involves feed-forward regulation by E(spl)/Hes genes. PLoS Genet (2013) 1.03
Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proc Natl Acad Sci U S A (2014) 1.00
Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. Proc Natl Acad Sci U S A (2013) 0.99
Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis. Plant Cell (2014) 0.92
Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to 'Candidatus Liberibacter asiaticus' infection. BMC Genomics (2013) 0.92
Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in maize. Plant Physiol (2011) 0.90
An RNA sequencing transcriptome analysis reveals novel insights into molecular aspects of the nitrate impact on the nodule activity of Medicago truncatula. Plant Physiol (2013) 0.90
AtNIGT1/HRS1 integrates nitrate and phosphate signals at the Arabidopsis root tip. Nat Commun (2015) 0.90
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics (2013) 0.88
Nitrate foraging by Arabidopsis roots is mediated by the transcription factor TCP20 through the systemic signaling pathway. Proc Natl Acad Sci U S A (2014) 0.88
A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Res (2013) 0.87
Nitrate sensing by the maize root apex transition zone: a merged transcriptomic and proteomic survey. J Exp Bot (2015) 0.87
Suppression of Arbuscule Degeneration in Medicago truncatula phosphate transporter4 Mutants is Dependent on the Ammonium Transporter 2 Family Protein AMT2;3. Plant Cell (2015) 0.86
Glucose elevates NITRATE TRANSPORTER2.1 protein levels and nitrate transport activity independently of its HEXOKINASE1-mediated stimulation of NITRATE TRANSPORTER2.1 expression. Plant Physiol (2013) 0.85
Root systems biology: integrative modeling across scales, from gene regulatory networks to the rhizosphere. Plant Physiol (2013) 0.85
Gene regulatory networks in plants: learning causality from time and perturbation. Genome Biol (2013) 0.84
Nitrogen metabolism of two contrasting poplar species during acclimation to limiting nitrogen availability. J Exp Bot (2013) 0.83
Dissection of the control of anion homeostasis by associative transcriptomics in Brassica napus. Plant Physiol (2014) 0.82
Plasmodesmata "in Communicado". Front Plant Sci (2012) 0.82
Common and specific responses to availability of mineral nutrients and water. J Exp Bot (2015) 0.81
Learning from Co-expression Networks: Possibilities and Challenges. Front Plant Sci (2016) 0.81
ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks. BMC Plant Biol (2014) 0.81
Nitrate regulation of AFB3 and NAC4 gene expression in Arabidopsis roots depends on NRT1.1 nitrate transport function. Plant Signal Behav (2014) 0.80
Development of the Poplar-Laccaria bicolor Ectomycorrhiza Modifies Root Auxin Metabolism, Signaling, and Response. Plant Physiol (2015) 0.80
From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks. Trends Genet (2015) 0.79
The Arabidopsis NRG2 Protein Mediates Nitrate Signaling and Interacts with and Regulates Key Nitrate Regulators. Plant Cell (2016) 0.79
"Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run". BMC Genomics (2016) 0.79
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. BMC Bioinformatics (2016) 0.78
Two short sequences in OsNAR2.1 promoter are necessary for fully activating the nitrate induced gene expression in rice roots. Sci Rep (2015) 0.78
Nitrogen-driven stem elongation in poplar is linked with wood modification and gene clusters for stress, photosynthesis and cell wall formation. BMC Plant Biol (2014) 0.77
Short-Term Molecular Acclimation Processes of Legume Nodules to Increased External Oxygen Concentration. Front Plant Sci (2016) 0.77
Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice. Plant Physiol (2015) 0.77
NPKS uptake, sensing, and signaling and miRNAs in plant nutrient stress. Protoplasma (2015) 0.76
Metabolic and co-expression network-based analyses associated with nitrate response in rice. BMC Genomics (2014) 0.76
Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. Front Plant Sci (2013) 0.76
A matter of time - How transient transcription factor interactions create dynamic gene regulatory networks. Biochim Biophys Acta (2016) 0.76
Transporters Involved in Root Nitrate Uptake and Sensing by Arabidopsis. Front Plant Sci (2016) 0.76
BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference. BMC Bioinformatics (2015) 0.76
Interacting TCP and NLP transcription factors control plant responses to nitrate availability. Proc Natl Acad Sci U S A (2017) 0.76
UMAMIT14 is an amino acid exporter involved in phloem unloading in Arabidopsis roots. J Exp Bot (2016) 0.75
Recent Advances in Understanding the Molecular Mechanisms Regulating the Root System Response to Phosphate Deficiency in Arabidopsis. Curr Genomics (2016) 0.75
A new insight into root responses to external cues: Paradigm shift in nutrient sensing. Plant Signal Behav (2015) 0.75
Dancing with Hormones: A Current Perspective of Nitrate Signaling and Regulation in Arabidopsis. Front Plant Sci (2017) 0.75
Reverse engineering highlights potential principles of large gene regulatory network design and learning. NPJ Syst Biol Appl (2017) 0.75
An Arabidopsis MADS box gene that controls nutrient-induced changes in root architecture. Science (1998) 5.80
The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell (2009) 5.52
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol (2006) 5.22
Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol (2004) 4.99
miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell (2009) 4.95
Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell (2006) 4.87
CHL1 functions as a nitrate sensor in plants. Cell (2009) 4.20
Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1,000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiol (2003) 4.14
Nitrate: nutrient and signal for plant growth. Plant Cell (1995) 4.14
Validating clustering for gene expression data. Bioinformatics (2001) 4.14
Nitrate-regulated auxin transport by NRT1.1 defines a mechanism for nutrient sensing in plants. Dev Cell (2010) 3.44
Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. Plant Cell (2000) 3.43
A predictive model for transcriptional control of physiology in a free living cell. Cell (2007) 3.35
Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A (2008) 3.17
Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol (2009) 2.98
Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell (2008) 2.87
The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol Biol (2008) 2.62
Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol (2004) 2.57
Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (2006) 2.49
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol (2007) 2.45
The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches. Proc Natl Acad Sci U S A (2006) 2.41
A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics (2004) 2.38
Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plant Physiol (2009) 2.33
Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. Plant Cell (2009) 1.66
Nitrate signaling: adaptation to fluctuating environments. Curr Opin Plant Biol (2010) 1.57
AtCIPK8, a CBL-interacting protein kinase, regulates the low-affinity phase of the primary nitrate response. Plant J (2008) 1.51
Plant hormones and nutrient signaling. Plant Mol Biol (2008) 1.51
A systems view of nitrogen nutrient and metabolite responses in Arabidopsis. Curr Opin Plant Biol (2008) 1.48
The nodule inception-like protein 7 modulates nitrate sensing and metabolism in Arabidopsis. Plant J (2008) 1.46
Transcript profiling in the chl1-5 mutant of Arabidopsis reveals a role of the nitrate transporter NRT1.1 in the regulation of another nitrate transporter, NRT2.1. Plant Cell (2004) 1.45
Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLA. Plant Mol Biol (2007) 1.39
Grouped graphical Granger modeling for gene expression regulatory networks discovery. Bioinformatics (2009) 1.35
Regulation of the high-affinity NO3- uptake system by NRT1.1-mediated NO3- demand signaling in Arabidopsis. Plant Physiol (2006) 1.19
A genetic screen for nitrate regulatory mutants captures the nitrate transporter gene NRT1.1. Plant Physiol (2009) 1.17
Insights into the genomic nitrate response using genetics and the Sungear Software System. J Exp Bot (2007) 1.16
Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula. Plant Physiol (2008) 1.13
Oxidative pentose phosphate pathway-dependent sugar sensing as a mechanism for regulation of root ion transporters by photosynthesis. Plant Physiol (2008) 1.10
Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst Biol (2009) 1.06
Modeling genetic regulatory dynamics in neural development. J Comput Biol (2001) 1.04
A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule". BMC Syst Biol (2009) 1.01
A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. PLoS Comput Biol (2009) 1.00
A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling. Plant Physiol (2009) 0.96
The effect of Glc6P uptake and its subsequent oxidation within pea root plastids on nitrite reduction and glutamate synthesis. J Exp Bot (2007) 0.85
An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis. BMC Syst Biol (2010) 0.79
A gene expression map of the Arabidopsis root. Science (2003) 9.95
Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A (2008) 3.17
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol (2007) 2.45
Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci U S A (2008) 2.17
Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2010) 2.03
OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics (2006) 1.90
VirtualPlant: a software platform to support systems biology research. Plant Physiol (2009) 1.88
Toward automatic phenotyping of developing embryos from videos. IEEE Trans Image Process (2005) 1.58
Nitrate signaling: adaptation to fluctuating environments. Curr Opin Plant Biol (2010) 1.57
Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants. Genome Biol (2004) 1.53
Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand. Proc Natl Acad Sci U S A (2011) 1.46
Genome-wide investigation of light and carbon signaling interactions in Arabidopsis. Genome Biol (2004) 1.44
Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana. Mol Biol Evol (2002) 1.33
Light- and carbon-signaling pathways. Modeling circuits of interactions. Plant Physiol (2003) 1.29
Overexpression of the ASN1 gene enhances nitrogen status in seeds of Arabidopsis. Plant Physiol (2003) 1.28
ESTimating plant phylogeny: lessons from partitioning. BMC Evol Biol (2006) 1.24
Overexpression of cytosolic glutamine synthetase. Relation to nitrogen, light, and photorespiration. Plant Physiol (2002) 1.19
A framework integrating plant growth with hormones and nutrients. Trends Plant Sci (2011) 1.19
Insights into the genomic nitrate response using genetics and the Sungear Software System. J Exp Bot (2007) 1.16
Systems biology for the virtual plant. Plant Physiol (2005) 1.11
Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biol (2003) 1.08
Correlation of ASN2 gene expression with ammonium metabolism in Arabidopsis. Plant Physiol (2003) 1.06
The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS One (2009) 1.06
Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway. Plant J (2002) 1.04
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. BMC Syst Biol (2008) 1.02
A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule". BMC Syst Biol (2009) 1.01
A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis. PLoS Comput Biol (2009) 1.00
Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. Proc Natl Acad Sci U S A (2013) 0.99
EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics (2005) 0.98
Achieving the in silico plant. Systems biology and the future of plant biological research. Plant Physiol (2003) 0.97
A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling. Plant Physiol (2009) 0.96
Molecular and physiological analysis of Arabidopsis mutants defective in cytosolic or chloroplastic aspartate aminotransferase. Plant Physiol (2002) 0.95
Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biol Evol (2010) 0.93
Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis. BMC Syst Biol (2010) 0.92
Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics (2006) 0.92
TARGET: a transient transformation system for genome-wide transcription factor target discovery. Mol Plant (2013) 0.89
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. BMC Genomics (2013) 0.88
Plasticity regulators modulate specific root traits in discrete nitrogen environments. PLoS Genet (2013) 0.87
RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis. Plant Physiol (2013) 0.85
A mutation in the Proteosomal Regulatory Particle AAA-ATPase-3 in Arabidopsis impairs the light-specific hypocotyl elongation response elicited by a glutamate receptor agonist, BMAA. Plant Mol Biol (2009) 0.83
High nitrogen insensitive 9 (HNI9)-mediated systemic repression of root NO3- uptake is associated with changes in histone methylation. Proc Natl Acad Sci U S A (2011) 0.81
Predicting genome-wide redundancy using machine learning. BMC Evol Biol (2010) 0.79
Rational design of temperature-sensitive alleles using computational structure prediction. PLoS One (2011) 0.78
In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana. BMC Bioinformatics (2009) 0.78
Transmeningeal muscimol can prevent focal EEG seizures in the rat neocortex without stopping multineuronal activity in the treated area. Brain Res (2011) 0.78
Plant systems biology: lessons from a fruitful collaboration. Plant Physiol (2003) 0.77
Effects of subdural application of lidocaine in patients with focal epilepsy. Epilepsy Res (2008) 0.77